The equation that describes the effect of phase relation of the sequence images on the super resolution image reconstruction was summarized. The amplification of Gaussian noise and shot-noise raised by super resolution image reconstruction was studied. Wiener Filter can restrain the amplified Gaussian noise effectively after super resolution image reconstruction. The shot noise, however, becomes ripple noise after image reconstruction. This brings image confusion because that traditional median filter can not restrain the ripple noise. Considering that the images processed are in sequence, a method of median filter based on sequence images was proposed. The pixels with noise, determined by pleonastic information in sequence images, were eliminated by median filter while the pixels without noise were kept untouched. Median filter based on sequence images restrains noise more powerfully than the one based on single image. It does not bring image confusion and thus improves the quality of the image.